2-25345310-A-G

Variant names:

• chr2-25345310-A-G
• rs36012910

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0393 in 152,346 control chromosomes in the GnomAD database, including 156 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.039 (156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5994 AN: 152228 Hom.: 156 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0277

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.0798

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0368

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0393 AC: 5994 AN: 152346 Hom.: 156 Cov.: 32 AF XY: 0.0394 AC XY: 2935 AN XY: 74496

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0277

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.0379

Gnomad4 SAS AF: 0.0797

Gnomad4 FIN AF: 0.0469

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.0180 Hom.: 6

Bravo AF: 0.0359

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs36012910; hg19: chr2-25568179;